How to use BASIC and Opentrons OT-2 to build an accurate, cost-effective, automated DNA assembly platform for synthetic biology.

To explore biology more deeply and faster, scientists need simple and efficient ways to build DNA structures.

"To develop new biological systems more efficiently, we are trying to apply engineering methods to biology."Imperial Geoff Baldwin, co-director of the Faculty's Center for Synthetic Biology, said: "From past experience, Make new DNA Structuring is a long process, usually taking two to three months—and it can fail along the way." So Baldwin and his colleaguesMarko Storch. and London Biofoundry Automation Lead Postdoctoral ResearcherMatt Haines Work together to develop a tool that makes building DNA easier and faster.

(Left to right) Matt Haines and Geoff Baldwin in their laboratory with the OT-2 liquid handling laboratory robot. Image source: Imperial College London

We've made some tooling improvements. "Today, we have better tools," says Baldwin, "and just like how you build IKEA furniture, you can build a biological system out of standard parts in a much more efficient way."

"Just like how you build IKEA furniture, you can build a biological system out of standard parts in a much more efficient way."

Getting to the Basics Before embarking on the automation project, Storch, Baldwin and other colleagues developed BASIC, primarily to standardize the assembly of biological parts for idempotent cloning. In part, BASIC prompted researchers to think in new ways about building DNA structures. "It provides excellent operability," says Baldwin. "Once you embrace a standardized approach, there's a tremendous freedom of thought. You no longer have to think about the details of individual sequences, overlaps, PCRs, etc."

In part, BASIC prompted researchers to think about building DNA constructs in new ways. "It provides excellent maneuverability," Baldwin said. “Once you embrace a standardized approach, there is greater freedom for self-examination—you no longer have to think about the details of individual sequences, overlaps, PCRs, etc.”

So, with BASIC, scientists shifted their attention from how to build DNA to thinking about the behavior of the system. Furthermore, the DNA constructs produced by BASIC are very accurate. "You have confidence that the synthetic DNA is what you want," says Baldwin.

With BASIC, scientists shifted their focus from how to build DNA to thinking about how the system behaves, while generating very accurate DNA constructs.

In addition to improving accuracy, BASIC simplifies the process of building DNA. "It provides an easier way to achieve DNA construction," Storch said. "You get the parts and connectors right out of the box, and there's no troubleshooting required." The scientists then just need to know how to combine part-connector-part-connector and so on to build a structure.

Baldwin compares this to the evolution of computers. A few decades ago, people building computers needed to know transistors and logic gates. "Today, you don't have to worry about the physics of computing because you can take the components right out of the box," he said. "Similarly, BASIC allows users to enjoy a similar level of abstraction as DNA."

However, getting the most out of BASIC also requires laboratory automation.

Adding Opentrons “When Opentrons launched OT-2, Opentrons’ open source philosophy really aligned with how we viewed the linker-based DNA assembly project,” said Storch. “Magnetic modules and temperature control The module provides the functionality we need."

Therefore, open source BASIC technology (available for free on GitHub) is ideally suited for use in open source automated pipetting robots Used on OT-2. "We believe the value of experimentation should be in what you build, not how you build it," Baldwin said. This gave rise to the DNA-BOT, an OT-2 capable of running BASIC.

(L-R) Matt Haines and Geoff Baldwin think about their DNA-Bot. Image source: Imperial College London

When asked about the advantages of running DNA-BOT, Haines said, "The first is cost-effectiveness." He then also highlighted the efficiency and accuracy of the method. “We obtained a construction of 88 components in each case, which was very efficient and achieved high accuracy,” he said. “This is difficult to achieve with non-standardized methods.”

At Imperial College London's Center for Synthetic Biology, Baldwin and colleagues set up a lab of six DNA-BOTs. “We’re trying to see if master’s students can use this platform to build structures,” Storch said.

Graduate students are setting up Imperial College Biofoundry. Image source: Imperial College London

Regardless of the results of these students' experiments, Baldwin's team already knows that DNA-BOT is a game-changer. "The design space we can explore is hundreds, if not thousands, of DNA structures," Baldwin said, "and it can quickly increase to tens of thousands."

As Haines emphasizes, "There's still a lot of variability to explore."

Enhance the applicationBaldwin's team sees more work to do. They've seen DNA-BOT work in a variety of applications, including studying existing biosynthetic pathways and creating new ones to build hard-to-make compounds.

The team will continue to develop and fine-tune DNA-BOT and plans to integrate Opentrons Thermocycler. “We want to build an ecosystem,” Baldwin said. “Create a DNA part and process that will empower your team members.” When affordable, easy-to-use, and efficient automation are combined with an advanced synthetic biology toolbox, the entire industry of building DNA structures will change, allowing virtually any Anyone can explore it.

References:

1. Storch, M., Haines, M.C., Baldwin, G.S. 2019. DNA-BOT: 合成生物學(xué)中低成本的可能性、自動化的DNA組裝平臺鍛造。bioRxiv. doi: http://stuff.do i.org/10.1101/832139.
2. Storch, M., Casini, A., Mackrow, B., et al. 2015. BASIC: a new biological component assembly standard for homomorphic cloning for synthetic biology, providing accurate, single-layer DNA assembly for synthetic biology , ACS Synth. Biol. 4:781–787.